I think the EU is saying, "On the one hand there are the WA and TCA; they are legal documents already agreed to by the UK government; and scrapping them, even by A.16, would unavoidably scrap both the form and the function of UK-EU relations.  On the other hand the NI Protocol Bill, while potentially a breach of the WA and probably the TCA as well, is still at this point only a piece of proposed legislation within a non-member state, and we're just going to let the people in the UK connect those dots of implication on their own rather than handing the crack-headed Brexiteers more ammunition for their accusation that the EU is trying to control the UK's internal affairs."